Yeah rnolan, I am running the same setup you have...through the MXC, Continuous Controller, and pedal, though I have two of them to run volume and wah. I reprogrammed the wah from pedal, to triggered and every which way possible (even when triggered halfway up the pedal) but the filter stays in the same position...its like it goes to instant Clapton woman tone, but in a bad way. Im glad the programming works as it should, but this is the only glitch in the entire preamp, and it might just be a loose connection (i'm a bit electronically challenged). It came like this when I unpacked it from an ebay purchase. Is seems as though I got fleeced for $250 plus potential repair costs but the guy incuded all the pedal gear along with it so maybe not so much. I'll try to get a hold of Marshall JMP for his opinion. Also, there is a rack mod tech at this link in Houston, near where I am, that I will go to for repair/modding:
http://www.thetonedoctor.com/default.html
http://www.thetonedoctor.com/Price-List-Shop-Online.html
BTW, anybody in the forums familiar with this guy?